PDB Short entry for 2MKD HEADER DNA BINDING PROTEIN 05-FEB-14 2MKD TITLE HUMAN JAZ ZF3 RESIDUES 168-227 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN 346; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 168-227; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZNF346, JAZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ZINC FINGER, DSRNA-BINDING, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.WRIGHT,J.DYSON,R.BURGE,M.MARTINEZ-YAMOUT REVDAT 3 14-JUN-23 2MKD 1 REMARK LINK REVDAT 2 26-MAR-14 2MKD 1 JRNL REVDAT 1 19-MAR-14 2MKD 0 JRNL AUTH R.G.BURGE,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT JRNL TITL STRUCTURAL CHARACTERIZATION OF INTERACTIONS BETWEEN THE JRNL TITL 2 DOUBLE-STRANDED RNA-BINDING ZINC FINGER PROTEIN JAZ AND JRNL TITL 3 NUCLEIC ACIDS. JRNL REF BIOCHEMISTRY V. 53 1495 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24521053 JRNL DOI 10.1021/BI401675H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000103718. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 55 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 200-300 MM [U-95% 13C; U-95% REMARK 210 15N] PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNCA; 3D HNCO; 3D HNCACB; 3D REMARK 210 1H-15N TOCSY; 3D 1H-13C NOESY; REMARK 210 3D HCCH-COSY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEW, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 7 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 224 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LYS A 170 152.13 65.40 REMARK 500 1 ALA A 173 -42.65 -152.21 REMARK 500 1 HIS A 175 95.18 -60.72 REMARK 500 1 GLN A 176 1.68 -68.55 REMARK 500 1 ARG A 178 -23.79 -146.60 REMARK 500 1 ARG A 224 47.15 -74.26 REMARK 500 2 ALA A 173 40.47 -72.46 REMARK 500 2 ARG A 178 -175.39 -69.13 REMARK 500 2 ASN A 195 32.34 -144.92 REMARK 500 2 ALA A 226 -149.07 49.49 REMARK 500 3 LYS A 170 -174.91 60.34 REMARK 500 3 GLU A 172 30.80 -142.61 REMARK 500 3 ASN A 177 -178.16 65.18 REMARK 500 3 TYR A 204 -5.44 -59.35 REMARK 500 3 LEU A 225 -11.00 -152.98 REMARK 500 3 ALA A 226 21.29 -143.68 REMARK 500 4 THR A 169 28.36 45.53 REMARK 500 4 GLU A 172 -168.65 60.21 REMARK 500 4 GLN A 176 5.81 53.09 REMARK 500 4 ASN A 177 51.04 -143.33 REMARK 500 4 GLU A 179 -174.02 -69.15 REMARK 500 5 ASN A 195 31.11 -140.46 REMARK 500 5 ALA A 226 26.69 -144.36 REMARK 500 6 VAL A 171 -25.22 -146.34 REMARK 500 6 LEU A 174 -54.80 -158.82 REMARK 500 6 HIS A 175 -35.54 -144.03 REMARK 500 6 ASN A 195 24.90 -142.35 REMARK 500 6 TYR A 204 -9.56 -57.71 REMARK 500 6 ALA A 226 5.05 -150.11 REMARK 500 7 LEU A 225 -42.96 -150.73 REMARK 500 8 GLU A 172 -56.71 -139.41 REMARK 500 8 ARG A 178 -172.93 61.18 REMARK 500 8 GLU A 179 37.43 -97.68 REMARK 500 8 ASN A 195 17.75 -140.38 REMARK 500 9 ASN A 177 -31.83 -156.69 REMARK 500 9 ALA A 226 -32.33 -156.83 REMARK 500 10 VAL A 171 -71.05 -133.44 REMARK 500 10 ASN A 177 46.42 -145.27 REMARK 500 10 ASN A 195 19.58 -140.03 REMARK 500 11 VAL A 171 46.69 -89.85 REMARK 500 11 LEU A 174 -44.25 -157.44 REMARK 500 12 LEU A 174 17.31 -142.45 REMARK 500 12 GLU A 179 -154.85 56.50 REMARK 500 12 ASN A 195 33.42 -144.61 REMARK 500 13 HIS A 175 45.42 -140.21 REMARK 500 13 ALA A 226 -11.12 -147.08 REMARK 500 14 ASN A 177 36.50 -84.47 REMARK 500 14 ASP A 182 66.34 -117.25 REMARK 500 14 ALA A 226 -30.68 57.55 REMARK 500 15 VAL A 171 29.52 -140.10 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 187 SG REMARK 620 2 CYS A 190 SG 109.8 REMARK 620 3 HIS A 203 NE2 112.6 108.3 REMARK 620 4 HIS A 209 ND1 109.5 110.0 106.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17679 RELATED DB: BMRB DBREF 2MKD A 168 227 UNP Q9UL40 ZN346_HUMAN 168 227 SEQRES 1 A 60 SER THR LYS VAL GLU ALA LEU HIS GLN ASN ARG GLU MET SEQRES 2 A 60 ILE ASP PRO ASP LYS PHE CYS SER LEU CYS HIS ALA THR SEQRES 3 A 60 PHE ASN ASP PRO VAL MET ALA GLN GLN HIS TYR VAL GLY SEQRES 4 A 60 LYS LYS HIS ARG LYS GLN GLU THR LYS LEU LYS LEU MET SEQRES 5 A 60 ALA ARG TYR GLY ARG LEU ALA ASP HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 196 TYR A 204 1 9 HELIX 2 2 GLY A 206 GLY A 223 1 18 SHEET 1 A 2 LYS A 185 CYS A 187 0 SHEET 2 A 2 ALA A 192 PHE A 194 -1 O PHE A 194 N LYS A 185 LINK SG CYS A 187 ZN ZN A 301 1555 1555 2.27 LINK SG CYS A 190 ZN ZN A 301 1555 1555 2.25 LINK NE2 HIS A 203 ZN ZN A 301 1555 1555 2.07 LINK ND1 HIS A 209 ZN ZN A 301 1555 1555 2.07 SITE 1 AC1 4 CYS A 187 CYS A 190 HIS A 203 HIS A 209 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000